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Bos taurus (taurine) and Bos indicus (indicine) cattle diverged at least 150,000 years ago and, since that time, substantial genomic differences have evolved between the two lineages. During the last two millennia, genetic exchange in Africa has resulted in a complex tapestry of taurine-indicine ancestry, with most cattle populations exhibiting varying levels of admixture. Similarly, there are several Southern European cattle populations that also show evidence for historical gene flow from indicine cattle, the highest levels of which are found in the Central Italian White breeds. Here we use two different software tools (MOSAIC and ELAI) for local ancestry inference (LAI) with genome-wide high- and low-density SNP array data sets in hybrid African and residually admixed Southern European cattle populations and obtained broadly similar results despite critical differences in the two LAI methodologies used. Our analyses identified genomic regions with elevated levels of retained or introgressed ancestry from the African taurine, European taurine, and Asian indicine lineages. Functional enrichment of genes underlying these ancestry peaks highlighted biological processes relating to immunobiology and olfaction, some of which may relate to differing susceptibilities to infectious diseases, including bovine tuberculosis, East Coast fever, and tropical theileriosis. Notably, for retained African taurine ancestry in admixed trypanotolerant cattle we observed enrichment of genes associated with haemoglobin and oxygen transport. This may reflect positive selection of genomic variants that enhance control of severe anaemia, a debilitating feature of trypanosomiasis disease, which severely constrains cattle agriculture across much of sub-Saharan Africa., Competing Interests: Competing interests: The authors declare no competing interests. Research Ethics Statement: For this study new Illumina® BovineHD 777 K BeadChip SNP data sets were generated for 39 individuals (23 Somba, 8 N’Dama and 8 Boran). The Somba individuals were obtained from DNA samples that were previously published as part of microsatellite-based surveys of cattle genetic diversity in the early 1990s and the N’Dama and Boran individuals were obtained from unpublished DNA samples collected during a time-course infection experiment carried out in 2003. This livestock DNA sampling work was completed prior to the requirement for Institutional Permission in Ireland, which is based on European Union Directive 2010/63/EU; however, all efforts were made to ensure ethical handling of all animal subjects., (© 2024. The Author(s), under exclusive licence to The Genetics Society.)

Background: Social network analysis of animal societies allows scientists to test hypotheses about social evolution, behaviour, and dynamic processes. However, the accuracy of estimated metrics depends on data characteristics like sample proportion, sample size, and frequency. A protocol is needed to assess for bias and robustness of social network metrics estimated for the animal populations especially when a limited number of individuals are monitored., Methods: We used GPS telemetry datasets of five ungulate species to combine known social network approaches with novel ones into a comprehensive five-step protocol. To quantify the bias and uncertainty in the network metrics obtained from a partial population, we presented novel statistical methods which are particularly suited for autocorrelated data, such as telemetry relocations. The protocol was validated using a sixth species, the fallow deer, with a known population size where ∼ 85 % of the individuals have been directly monitored., Results: Through the protocol, we demonstrated how pre-network data permutations allow researchers to assess non-random aspects of interactions within a population. The protocol assesses bias in global network metrics, obtains confidence intervals, and quantifies uncertainty of global and node-level network metrics based on the number of nodes in the network. We found that global network metrics like density remained robust even with a lowered sample size, while local network metrics like eigenvector centrality were unreliable for four of the species. The fallow deer network showed low uncertainty and bias even at lower sampling proportions, indicating the importance of a thoroughly sampled population while demonstrating the accuracy of our evaluation methods for smaller samples., Conclusions: The protocol allows researchers to analyse GPS-based radio-telemetry or other data to determine the reliability of social network metrics. The estimates enable the statistical comparison of networks under different conditions, such as analysing daily and seasonal changes in the density of a network. The methods can also guide methodological decisions in animal social network research, such as sampling design and allow more accurate ecological inferences from the available data. The R package aniSNA enables researchers to implement this workflow on their dataset, generating reliable inferences and guiding methodological decisions., (© 2024. The Author(s).)

The UK Biobank (UKB) is a large cohort study that recruited over 500,000 British participants aged 40-69 in 2006-2010 at 22 assessment centers from across the United Kingdom. Self-reported health outcomes and hospital admission data are 2 types of records that include participants' disease status. Coronary artery disease (CAD) is the most common cause of death in the UKB cohort. After distinguishing between prevalence and incidence CAD events for all UKB participants, we identified geographical variations in age-standardized rates of CAD between assessment centers. Significant distributional differences were found between the pooled cohort equation scores of UKB participants from England and Scotland using the Mann-Whitney test. Polygenic risk scores of UKB participants from England and Scotland and from different assessment centers differed significantly using permutation tests. Our aim was to discriminate between assessment centers with different disease rates by collecting data on disease-related risk factors. However, relying solely on individual-level predictions and averaging them to obtain group-level predictions proved ineffective, particularly due to the presence of correlated covariates resulting from participation bias. By using the Mundlak model, which estimates a random effects regression by including the group means of the independent variables in the model, we effectively addressed these issues. In addition, we designed a simulation experiment to demonstrate the functionality of the Mundlak model. Our findings have applications in public health funding and strategy, as our approach can be used to predict case rates in the future, as both population structure and lifestyle changes are uncertain., Competing Interests: Conflicts of interest The author(s) declare no conflicts of interest., (© The Author(s) 2024. Published by Oxford University Press on behalf of The Genetics Society of America.)

Zoonotic diseases represent a significant societal challenge in terms of their health and economic impacts. One Health approaches to managing zoonotic diseases are becoming more prevalent, but require novel thinking, tools and cross-disciplinary collaboration. Bovine tuberculosis (bTB) is one example of a costly One Health challenge with a complex epidemiology involving humans, domestic animals, wildlife and environmental factors, which require sophisticated collaborative approaches. We undertook a scoping review of multi-host bTB epidemiology to identify trends in species publication focus, methodologies, and One Health approaches. We aimed to identify knowledge gaps where novel research could provide insights to inform control policy, for bTB and other zoonoses. The review included 532 articles. We found different levels of research attention across episystems, with a significant proportion of the literature focusing on the badger-cattle-TB episystem, with far less attention given to tropical multi-host episystems. We found a limited number of studies focusing on management solutions and their efficacy, with very few studies looking at modelling exit strategies. Only a small number of studies looked at the effect of human disturbances on the spread of bTB involving wildlife hosts. Most of the studies we reviewed focused on the effect of badger vaccination and culling on bTB dynamics with few looking at how roads, human perturbations and habitat change may affect wildlife movement and disease spread. Finally, we observed a lack of studies considering the effect of weather variables on bTB spread, which is particularly relevant when studying zoonoses under climate change scenarios. Significant technological and methodological advances have been applied to bTB episystems, providing explicit insights into its spread and maintenance across populations. We identified a prominent bias towards certain species and locations. Generating more high-quality empirical data on wildlife host distribution and abundance, high-resolution individual behaviours and greater use of mathematical models and simulations are key areas for future research. Integrating data sources across disciplines, and a "virtuous cycle" of well-designed empirical data collection linked with mathematical and simulation modelling could provide additional gains for policy-makers and managers, enabling optimised bTB management with broader insights for other zoonoses., (© 2024. The Author(s).)

Criollo cattle, the descendants of animals brought by Iberian colonists to the Americas, have been the subject of natural and human-mediated selection in novel tropical agroecological zones for centuries. Consequently, these breeds have evolved distinct characteristics such as resistance to diseases and exceptional heat tolerance. In addition to European taurine ( Bos taurus ) ancestry, it has been proposed that gene flow from African taurine and Asian indicine ( Bos indicus ) cattle has shaped the ancestry of Criollo cattle. In this study, we analysed Criollo breeds from Colombia and Venezuela using whole-genome sequencing (WGS) and single-nucleotide polymorphism (SNP) array data to examine population structure and admixture at high resolution. Analysis of genetic structure and ancestry components provided evidence for African taurine and Asian indicine admixture in Criollo cattle. In addition, using WGS data, we detected selection signatures associated with a myriad of adaptive traits, revealing genes linked to thermotolerance, reproduction, fertility, immunity and distinct coat and skin coloration traits. This study underscores the remarkable adaptability of Criollo cattle and highlights the genetic richness and potential of these breeds in the face of climate change, habitat flux and disease challenges. Further research is warranted to leverage these findings for more effective and sustainable cattle breeding programmes., Competing Interests: We declare we have no competing interests., (© 2024 The Authors.)

Scientifically underpinning geographic origin claims will improve consumer trust in food labels. Stable isotope ratio analysis (SIRA) is an analytical technique that supports origin verification of food products based on naturally occurring differences in isotopic compositions. SIRA of five relevant elements (C, H, N, O, S) was conducted on casein isolated from butter (n = 60), cheese (n = 96), and whole milk powder (WMP) (n = 41). Samples were divided into four geographic regions based on their commercial origin: Ireland (n = 79), Europe (n = 67), Australasia (n = 29) and USA (n = 22). A random forest machine learning model built using δ 13 C, δ 2 H, δ 15 N, δ 18 O and δ 34 S values of all products (n = 197) accurately (88% model accuracy rate) predicted the region of origin with class accuracy of 95% for Irish, 84% for European, 71% for Australasia, and 94% for US products., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2023 The Author(s).)

The phenotypic diversity of African cattle reflects adaptation to a wide range of agroecological conditions, human-mediated selection preferences, and complex patterns of admixture between the humpless Bos taurus (taurine) and humped Bos indicus (zebu) subspecies, which diverged 150-500 thousand years ago. Despite extensive admixture, all African cattle possess taurine mitochondrial haplotypes, even populations with significant zebu biparental and male uniparental nuclear ancestry. This has been interpreted as the result of human-mediated dispersal ultimately stemming from zebu bulls imported from South Asia during the last three millennia. Here, we assess whether ancestry at mitochondrially targeted nuclear genes in African admixed cattle is impacted by mitonuclear functional interactions. Using high-density SNP data, we find evidence for mitonuclear coevolution across hybrid African cattle populations with a significant increase of taurine ancestry at mitochondrially targeted nuclear genes. Our results, therefore, support the hypothesis of incompatibility between the taurine mitochondrial genome and the zebu nuclear genome., Competing Interests: The authors declare no competing interest., (© 2022 The Author(s).)

Background: In bacteria, genes with related functions-such as those involved in the metabolism of the same compound or in infection processes-are often physically close on the genome and form groups called clusters. The enrichment of such clusters over various distantly related bacteria can be used to predict the roles of genes of unknown function that cluster with characterised genes. There is no obvious rule to define a cluster, given their variability in size and intergenic distances, and the definition of what comprises a "gene", since genes can gain and lose domains over time. Protein domains can cluster within a gene, or in adjacent genes of related function, and in both cases these are chromosomally clustered. Here, we model the distances between pairs of protein domain coding regions across a wide range of bacteria and archaea via a probabilistic two component mixture model, without imposing arbitrary thresholds in terms of gene numbers or distances., Results: We trained our model using matched gene ontology terms to label functionally related pairs and assess the stability of the parameters of the model across 14,178 archaeal and bacterial strains. We found that the parameters of our mixture model are remarkably stable across bacteria and archaea, except for endosymbionts and obligate intracellular pathogens. Obligate pathogens have smaller genomes, and although they vary, on average do not show noticeably different clustering distances; the main difference in the parameter estimates is that a far greater proportion of the genes sharing ontology terms are clustered. This may reflect that these genomes are enriched for complexes encoded by clustered core housekeeping genes, as a proportion of the total genes. Given the overall stability of the parameter estimates, we then used the mean parameter estimates across the entire dataset to investigate which gene ontology terms are most frequently associated with clustered genes., Conclusions: Given the stability of the mixture model across species, it may be used to predict bacterial gene clusters that are shared across multiple species, in addition to giving insights into the evolutionary pressures on the chromosomal locations of genes in different species., (© 2021. The Author(s).)

We present an algorithm for inferring ancestry segments and characterizing admixture events, which involve an arbitrary number of genetically differentiated groups coming together. This allows inference of the demographic history of the species, properties of admixing groups, identification of signatures of natural selection, and may aid disease gene mapping. The algorithm employs nested hidden Markov models to obtain local ancestry estimation along the genome for each admixed individual. In a range of simulations, the accuracy of these estimates equals or exceeds leading existing methods. Moreover, and unlike these approaches, we do not require any prior knowledge of the relationship between subgroups of donor reference haplotypes and the unseen mixing ancestral populations. Our approach infers these in terms of conditional "copying probabilities." In application to the Human Genome Diversity Project, we corroborate many previously inferred admixture events ( e.g. , an ancient admixture event in the Kalash). We further identify novel events such as complex four-way admixture in San-Khomani individuals, and show that Eastern European populations possess [Formula: see text] ancestry from a group resembling modern-day central Asians. We also identify evidence of recent natural selection favoring sub-Saharan ancestry at the human leukocyte antigen (HLA) region, across North African individuals. We make available an R and C++ software library, which we term MOSAIC (which stands for MOSAIC Organizes Segments of Ancestry In Chromosomes)., (Copyright © 2019 Salter-Townshend and Myers.)

Social relationships consist of interactions along multiple dimensions. In social networks, this means that individuals form multiple types of relationships with the same person (e.g., an individual will not trust all of his/her acquaintances). Statistical models for these data require understanding two related types of dependence structure: (i) structure within each relationship type, or network view, and (ii) the association between views. In this paper, we propose a statistical framework that parsimoniously represents dependence between relationship types while also maintaining enough flexibility to allow individuals to serve different roles in different relationship types. Our approach builds on work on latent space models for networks [see, e.g., J. Amer. Statist. Assoc. 97 (2002) 1090-1098]. These models represent the propensity for two individuals to form edges as conditionally independent given the distance between the individuals in an unobserved social space. Our work departs from previous work in this area by representing dependence structure between network views through a multivariate Bernoulli likelihood, providing a representation of between-view association. This approach infers correlations between views not explained by the latent space model. Using our method, we explore 6 multiview network structures across 75 villages in rural southern Karnataka, India [Banerjee et al. (2013)].

A novel and flexible framework for investigating the roles of actors within a network is introduced. Particular interest is in roles as defined by local network connectivity patterns, identified using the ego-networks extracted from the network. A mixture of Exponential-family Random Graph Models is developed for these ego-networks in order to cluster the nodes into roles. We refer to this model as the ego-ERGM. An Expectation-Maximization algorithm is developed to infer the unobserved cluster assignments and to estimate the mixture model parameters using a maximum pseudo-likelihood approximation. The flexibility and utility of the method are demonstrated on examples of simulated and real networks.